[package - main-amd64-default][biology/kallisto] Failed for kallisto-0.51.1,1 in build
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Date: Fri, 25 Oct 2024 17:18:47 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: jwb@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/p645a502a4f60_s8b2e7da7085/logs/kallisto-0.51.1,1.log
Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p645a502a4f60_s8b2e7da7085
Log:
=>> Building biology/kallisto
build started at Fri Oct 25 17:18:33 UTC 2024
port directory: /usr/ports/biology/kallisto
package name: kallisto-0.51.1,1
building for: FreeBSD main-amd64-default-job-04 15.0-CURRENT FreeBSD 15.0-CURRENT 1500026 amd64
maintained by: jwb@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 1446 Sep 21 01:01 /usr/ports/biology/kallisto/Makefile
Ports top last git commit: 645a502a4f6
Ports top unclean checkout: no
Port dir last git commit: c449c3e4774
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2
Host OSVERSION: 1500023
Jail OSVERSION: 1500026
Job Id: 04
!!! Jail is newer than host. (Jail: 1500026, Host: 1500023) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1500026
UNAME_v=FreeBSD 15.0-CURRENT 1500026
UNAME_r=15.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
MAKE_OBJDIR_CHECK_WRITABLE=0
LOCALBASE=/usr/local
USER=root
POUDRIERE_NAME=poudriere-git
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.4.2
MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
PWD=/usr/local/poudriere/data/.m/main-amd64-default/04/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=main-amd64-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.2
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for kallisto-0.51.1,1:
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
jwb@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/kallisto/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/kallisto/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/kallisto/work/.cache HOME=/wrkdirs/usr/ports/biology/kallisto/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/kallisto/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/kallisto/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local"
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/kallisto/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/kallisto/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/kallisto/work/.cache HOME=/wrkdirs/usr/ports/biology/kallisto/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/kallisto/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/kallisto/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lhts -lz -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " BSD_INSTALL_
PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
PORTEXAMPLES="" CMAKE_BUILD_TYPE="release" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/kallisto" EXAMPLESDIR="share/examples/kallisto" DATADIR="share/kallisto" WWWDIR="www/kallisto" ETCDIR="etc/kallisto"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/kallisto DOCSDIR=/usr/local/share/doc/kallisto EXAMPLESDIR=/usr/local/share/examples/kallisto WWWDIR=/usr/local/www/kallisto ETCDIR=/usr/local/etc/kallisto
--End SUB_LIST--
---Begin make.conf---
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
GID=0
UID=0
---End make.conf---
--Resource limits--
ulimit: can't get limit: Invalid argument
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 33554432
stack size (kbytes, -s) 524288
core file size (512-blocks, -c) unlimited
max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
max user processes (-u) 89999
open files (-n) 8192
virtual mem size (kbytes, -v) unlimited
swap limit (kbytes, -w) unlimited
socket buffer size (bytes, -b) unlimited
pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD2CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> kallisto-0.51.1,1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.3.pkg
[main-amd64-default-job-04] Installing pkg-1.21.3...
[main-amd64-default-job-04] Extracting pkg-1.21.3: .......... done
===> kallisto-0.51.1,1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of kallisto-0.51.1,1
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by kallisto-0.51.1,1 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by kallisto-0.51.1,1 for building
=> SHA256 Checksum OK for pachterlab-kallisto-v0.51.1_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by kallisto-0.51.1,1 for building
===> Extracting for kallisto-0.51.1,1
=> SHA256 Checksum OK for pachterlab-kallisto-v0.51.1_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Patching for kallisto-0.51.1,1
===> Applying FreeBSD patches for kallisto-0.51.1,1 from /usr/ports/biology/kallisto/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> kallisto-0.51.1,1 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.30.5.pkg
[main-amd64-default-job-04] Installing cmake-core-3.30.5...
[main-amd64-default-job-04] `-- Installing expat-2.6.3...
[main-amd64-default-job-04] `-- Extracting expat-2.6.3: .......... done
<snip>
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerCovIndex.tcc:80:63: note: while substituting into a lambda expression here
80 | auto copyBlock = [&](const size_t start, const size_t end){
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:94:16: note: in instantiation of member function 'KmerCovIndex<>::toData' requested here
94 | km_unitigs.toData(std::move(o.km_unitigs), nb_threads);
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:630:45: note: in instantiation of member function 'CompactedDBG<>::toDataGraph' requested here
630 | if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads);
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:609:36: note: in instantiation of member function 'CompactedDBG<>::build' requested here
609 | success = cdbg.build(opt);
| ^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:2771:31: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
2771 | if (reference_mode) bf2 = move(bf1);
| ^
| std::
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:696:76: note: in instantiation of member function 'CompactedDBG<>::filter' requested here
696 | pair<bool, pair<BlockedBloomFilter, Roaring>> filter_out = filter(opt, nb_unique_kmers, nb_non_unique_kmers);
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:609:36: note: in instantiation of member function 'CompactedDBG<>::build' requested here
609 | success = cdbg.build(opt);
| ^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2423:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
2423 | unitig = new Unitig<U>(move(cs), move(cc));
| ^
| std::
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:325:34: note: in instantiation of member function 'CompactedDBG<DataAccessor<>, DataStorage<>>::readGraphFromIndexFASTA' requested here
325 | p_readSuccess_checksum = readGraphFromIndexFASTA(input_graph_fn, input_index_fn, k_, g_);
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:167:16: note: in instantiation of member function 'CompactedDBG<DataAccessor<>, DataStorage<>>::read' requested here
167 | return read(input_graph_fn, input_index_fn, nb_threads, verbose);
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:612:61: note: in instantiation of member function 'CompactedDBG<DataAccessor<>, DataStorage<>>::read' requested here
612 | if (!CompactedDBG<DataAccessor<U>, DataStorage<U>>::read(input_graph_fn, nb_threads, verbose)) return false; // Read graph
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:623:80: note: in instantiation of member function 'ColoredCDBG<>::read' requested here
623 | if (lopt.filename_index_in.length() == 0) success = ccdbg1.read(lopt.filename_graph_in, lopt.filename_colors_in, lopt.nb_threads, lopt.verbose);
| ^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2423:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
2423 | unitig = new Unitig<U>(move(cs), move(cc));
| ^
| std::
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2534:44: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
2534 | unitig = new Unitig<U>(move(cs), move(cc));
| ^
| std::
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:378:34: note: in instantiation of member function 'CompactedDBG<DataAccessor<>, DataStorage<>>::readGraphFromIndexGFA' requested here
378 | p_readSuccess_checksum = readGraphFromIndexGFA(input_graph_fn, input_index_fn, k_, g_);
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:167:16: note: in instantiation of member function 'CompactedDBG<DataAccessor<>, DataStorage<>>::read' requested here
167 | return read(input_graph_fn, input_index_fn, nb_threads, verbose);
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:612:61: note: in instantiation of member function 'CompactedDBG<DataAccessor<>, DataStorage<>>::read' requested here
612 | if (!CompactedDBG<DataAccessor<U>, DataStorage<U>>::read(input_graph_fn, nb_threads, verbose)) return false; // Read graph
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:623:80: note: in instantiation of member function 'ColoredCDBG<>::read' requested here
623 | if (lopt.filename_index_in.length() == 0) success = ccdbg1.read(lopt.filename_graph_in, lopt.filename_colors_in, lopt.nb_threads, lopt.verbose);
| ^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2534:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
2534 | unitig = new Unitig<U>(move(cs), move(cc));
| ^
| std::
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1690:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
1690 | unitig = new Unitig<U>(move(cs), move(cc));
| ^
| std::
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1631:12: note: in instantiation of member function 'CompactedDBG<DataAccessor<>, DataStorage<>>::readBinaryGraph' requested here
1631 | return readBinaryGraph(in);
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:383:34: note: in instantiation of member function 'CompactedDBG<DataAccessor<>, DataStorage<>>::readBinaryGraph' requested here
383 | p_readSuccess_checksum = readBinaryGraph(input_graph_fn);
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:167:16: note: in instantiation of member function 'CompactedDBG<DataAccessor<>, DataStorage<>>::read' requested here
167 | return read(input_graph_fn, input_index_fn, nb_threads, verbose);
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:612:61: note: in instantiation of member function 'CompactedDBG<DataAccessor<>, DataStorage<>>::read' requested here
612 | if (!CompactedDBG<DataAccessor<U>, DataStorage<U>>::read(input_graph_fn, nb_threads, verbose)) return false; // Read graph
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:623:80: note: in instantiation of member function 'ColoredCDBG<>::read' requested here
623 | if (lopt.filename_index_in.length() == 0) success = ccdbg1.read(lopt.filename_graph_in, lopt.filename_colors_in, lopt.nb_threads, lopt.verbose);
| ^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1690:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
1690 | unitig = new Unitig<U>(move(cs), move(cc));
| ^
| std::
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:2:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.hpp:369:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:505:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
505 | *uc = move(r_uc);
| ^
| std::
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:481:81: note: while substituting into a lambda expression here
481 | auto join_function = [this](const vector<pair<Kmer, uint8_t>>& unitig_tags) {
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:616:14: note: in instantiation of member function 'ColoredCDBG<>::loadColors' requested here
616 | if (!loadColors(input_graph_fn, input_colors_fn, nb_threads, verbose)) return false;
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:623:80: note: in instantiation of member function 'ColoredCDBG<>::read' requested here
623 | if (lopt.filename_index_in.length() == 0) success = ccdbg1.read(lopt.filename_graph_in, lopt.filename_colors_in, lopt.nb_threads, lopt.verbose);
| ^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:2:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.hpp:369:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:225:87: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
225 | const bool ret = CompactedDBG<DataAccessor<U>, DataStorage<U>>::mergeData(move(o), nb_threads, verbose);
| ^
| std::
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:644:60: note: in instantiation of member function 'ColoredCDBG<>::merge' requested here
644 | if (success) success = ccdbg_a.merge(move(ccdbg_b), lopt.nb_threads, lopt.verbose);
| ^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2423:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
2423 | unitig = new Unitig<U>(move(cs), move(cc));
| ^
| std::
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:325:34: note: in instantiation of member function 'CompactedDBG<>::readGraphFromIndexFASTA' requested here
325 | p_readSuccess_checksum = readGraphFromIndexFASTA(input_graph_fn, input_index_fn, k_, g_);
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:656:42: note: in instantiation of member function 'CompactedDBG<>::read' requested here
656 | else success = cdbg1.read(lopt.filename_graph_in, lopt.filename_index_in, lopt.nb_threads, lopt.verbose);
| ^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2423:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
2423 | unitig = new Unitig<U>(move(cs), move(cc));
| ^
| std::
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2534:44: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
2534 | unitig = new Unitig<U>(move(cs), move(cc));
| ^
| std::
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:378:34: note: in instantiation of member function 'CompactedDBG<>::readGraphFromIndexGFA' requested here
378 | p_readSuccess_checksum = readGraphFromIndexGFA(input_graph_fn, input_index_fn, k_, g_);
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:656:42: note: in instantiation of member function 'CompactedDBG<>::read' requested here
656 | else success = cdbg1.read(lopt.filename_graph_in, lopt.filename_index_in, lopt.nb_threads, lopt.verbose);
| ^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2534:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
2534 | unitig = new Unitig<U>(move(cs), move(cc));
| ^
| std::
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1690:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
1690 | unitig = new Unitig<U>(move(cs), move(cc));
| ^
| std::
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1631:12: note: in instantiation of member function 'CompactedDBG<>::readBinaryGraph' requested here
1631 | return readBinaryGraph(in);
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:383:34: note: in instantiation of member function 'CompactedDBG<>::readBinaryGraph' requested here
383 | p_readSuccess_checksum = readBinaryGraph(input_graph_fn);
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:656:42: note: in instantiation of member function 'CompactedDBG<>::read' requested here
656 | else success = cdbg1.read(lopt.filename_graph_in, lopt.filename_index_in, lopt.nb_threads, lopt.verbose);
| ^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1690:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
1690 | unitig = new Unitig<U>(move(cs), move(cc));
| ^
| std::
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:2:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.hpp:369:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:1758:55: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
1758 | buffers_seq.push_back(move(s));
| ^
| std::
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:1726:20: note: while substituting into a lambda expression here
1726 | [&]{
| ^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:696:50: note: in instantiation of member function 'ColoredCDBG<>::search' requested here
696 | if (success) success = ccdbg.search(opt.filename_query_in, opt.prefixFilenameOut, opt.ratio_kmers, opt.inexact_search, opt.nb_threads, opt.verbose);
| ^
68 warnings and 1 error generated.
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